› 3pmh

X-ray diffraction
3.2Å resolution

Mechanism of Sulfotyrosine-Mediated Glycoprotein Ib Interaction with Two Distinct alpha-Thrombin Sites

Released:
DOI: 10.2210/pdb3pmh/pdb
PDB entry 3pmh coloured by chain, front view.
PDB entry 3pmh coloured by chain, side view.
PDB entry 3pmh coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Binding of alpha-thrombin to surface-anchored platelet glycoprotein Ib(alpha) sulfotyrosines through a two-site mechanism involving exosite I.
Zarpellon A, Celikel R, Roberts JR, McClintock RA, Mendolicchio GL, Moore KL, Jing H, Varughese KI, Ruggeri ZM
Proc Natl Acad Sci U S A 108 8628-33 (2011)
PMID: 21555542

Function and Biology Details

Reaction catalysed: 
Selective cleavage of Arg-|-Gly bonds in fibrinogen to form fibrin and release fibrinopeptides A and B.
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-133073 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (4 distinct):
Thrombin light chain Chain: A
Molecule details ›
Chain: A
Length: 36 amino acids
Theoretical weight: 4.1 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P00734 (Residues: 328-363; Coverage: 6%)
Gene name: F2
Sequence domains: Thrombin light chain
Thrombin heavy chain Chain: B
Molecule details ›
Chain: B
Length: 259 amino acids
Theoretical weight: 29.78 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P00734 (Residues: 364-622; Coverage: 43%)
Gene name: F2
Sequence domains: Trypsin
Structure domains: Trypsin-like serine proteases
Glycocalicin Chain: G
Molecule details ›
Chain: G
Length: 290 amino acids
Theoretical weight: 32.55 KDa
Source organism: Homo sapiens
Expression system: Drosophila melanogaster
UniProt:
  • Canonical: P07359 (Residues: 17-306; Coverage: 46%)
Gene name: GP1BA
Sequence domains:
Structure domains: Ribonuclease Inhibitor

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG, MAN
Carbohydrate polymer
2 bound ligands:
Ligand 0G7 1 x 0G7
Ligand NAG 1 x NAG
1 modified residue:
Ligand TYS 3 x TYS

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRL BEAMLINE BL9-2
Spacegroup: P43212
Unit cell:
a: 67.657Å b: 67.657Å c: 329.73Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.22 0.22 0.263
Expression system: Drosophila melanogaster

Quick links

Citations

7 review citations

von Willebrand factor, Jedi knight of the bloodstream.
Springer TA. (2014)
6 more

3 mentions without citation

GARP regulates the bioavailability and activation of TGFβ.
Wang et al. (2012)
2 more